October 2021 - petsc-dev - mailman3.cels.anl.gov

Big in MF hessian and BNK?
by Stefano Zampini 14 Oct '21

14 Oct '21

Alp I have found this problem, reproducible with release (see below using src/tao/unconstrained/tutorials/minsurf1) I was trying MFFD hessian with bntr. Using assembled hessian is fine (tf-oneapi) [szampini@localhost tutorials]$ ./minsurf1 -tao_smonitor -tao_type bntr -mx 10 -my 8 -tao_bnk_max_cg_its 3 -tao_gatol 1.e-4 ---- Minimum Surface Area Problem ----- mx: 10 my: 8 iter = 0, Function value 1.45591, Residual: 0.21372 iter = 0, Function value 1.43469, Residual: 0.205909 iter = 0, Function value 1.43469, Residual: 0.205909 iter = 1, Function value 1.42058, Residual: 0.0881207 iter = 2, Function value 1.41987, Residual: 0.10019 iter = 3, Function value 1.41797, Residual: 0.0209656 iter = 1, Function value 1.41775, Residual: 0.000288154 iter = 0, Function value 1.41775, Residual: 0.000288154 iter = 1, Function value 1.41775, Residual: 0.000207788 iter = 2, Function value 1.41775, Residual: 0.000123638 iter = 3, Function value 1.41775, Residual: 0.000117563 iter = 2, Function value 1.41775, Residual: < 1.0e-6 Using MFFD hessian error (using bnls segefaults, we should try to check all possible Tao solvers affected by this bug?) (tf-oneapi) [szampini@localhost tutorials]$ ./minsurf1 -tao_smonitor -tao_type bntr -mx 10 -my 8 -tao_bnk_max_cg_its 3 -tao_gatol 1.e-4 -tao_mf_hessian ---- Minimum Surface Area Problem ----- mx: 10 my: 8 iter = 0, Function value 1.45591, Residual: 0.21372 iter = 0, Function value 1.43469, Residual: 0.205909 iter = 0, Function value 1.43469, Residual: 0.205909 iter = 1, Function value 1.42058, Residual: 0.0881207 iter = 2, Function value 1.41987, Residual: 0.10019 iter = 3, Function value 1.41797, Residual: 0.0209656 [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Object is in wrong state [0]PETSC ERROR: MatMFFDSetBase() has not been called, this is often caused by forgetting to call MatAssemblyBegin/End on the first Mat in the SNES compute function [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.0, unknown [0]PETSC ERROR: ./minsurf1 on a arch-conda-tf-oneapi-single-real named localhost.localdomain by szampini Thu Oct 14 18:11:23 2021 [0]PETSC ERROR: Configure options --with-blaslapack-dir=/home/szampini/Devel/miniforge/envs/tf-oneapi --download-thrust --LDFLAGS=-liomp5 --with-debugging=0 --with-openmp --with-precision=single --with-fc=0 --download-h2opus --download-slepc --download-slepc-commit=origin/release PETSC_ARCH=arch-conda-tf-oneapi-single-real PETSC_DIR=/home/szampini/Devel/miniforge/Devel/petsc [0]PETSC ERROR: #1 MatMult_MFFD() at /home/szampini/Devel/miniforge/Devel/petsc/src/mat/impls/mffd/mffd.c:333 [0]PETSC ERROR: #2 MatMult_Shell() at /home/szampini/Devel/miniforge/Devel/petsc/src/mat/impls/shell/shell.c:1066 [0]PETSC ERROR: #3 MatMult() at /home/szampini/Devel/miniforge/Devel/petsc/src/mat/interface/matrix.c:2439 [0]PETSC ERROR: #4 KSP_MatMult() at /home/szampini/Devel/miniforge/Devel/petsc/include/petsc/private/kspimpl.h:346 [0]PETSC ERROR: #5 KSPCGSolve_STCG() at /home/szampini/Devel/miniforge/Devel/petsc/src/ksp/ksp/impls/cg/stcg/stcg.c:183 [0]PETSC ERROR: #6 KSPSolve_Private() at /home/szampini/Devel/miniforge/Devel/petsc/src/ksp/ksp/interface/itfunc.c:914 [0]PETSC ERROR: #7 KSPSolve() at /home/szampini/Devel/miniforge/Devel/petsc/src/ksp/ksp/interface/itfunc.c:1086 [0]PETSC ERROR: #8 TaoBNKComputeStep() at /home/szampini/Devel/miniforge/Devel/petsc/src/tao/bound/impls/bnk/bnk.c:477 [0]PETSC ERROR: #9 TaoSolve_BNTR() at /home/szampini/Devel/miniforge/Devel/petsc/src/tao/bound/impls/bnk/bntr.c:139 [0]PETSC ERROR: #10 TaoSolve() at /home/szampini/Devel/miniforge/Devel/petsc/src/tao/interface/taosolver.c:227 [0]PETSC ERROR: #11 main() at minsurf1.c:110 [0]PETSC ERROR: PETSc Option Table entries: [0]PETSC ERROR: -check_pointer_intensity 0 [0]PETSC ERROR: -mx 10 [0]PETSC ERROR: -my 8 [0]PETSC ERROR: -tao_bnk_max_cg_its 3 [0]PETSC ERROR: -tao_gatol 1.e-4 [0]PETSC ERROR: -tao_mf_hessian [0]PETSC ERROR: -tao_smonitor [0]PETSC ERROR: -tao_type bntr [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint(a)mcs.anl.gov---------- Abort(73) on node 0 (rank 0 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 73) - process 0 Using fd is fine (tf-oneapi) [szampini@localhost tutorials]$ ./minsurf1 -tao_smonitor -tao_type bntr -mx 10 -my 8 -tao_bnk_max_cg_its 3 -tao_gatol 1.e-4 -tao_fd_hessian ---- Minimum Surface Area Problem ----- mx: 10 my: 8 iter = 0, Function value 1.45591, Residual: 0.21372 iter = 0, Function value 1.43469, Residual: 0.205909 iter = 0, Function value 1.43469, Residual: 0.205909 iter = 1, Function value 1.42058, Residual: 0.0881207 iter = 2, Function value 1.41987, Residual: 0.10019 iter = 3, Function value 1.41797, Residual: 0.0209656 iter = 1, Function value 1.41775, Residual: 0.000342734 iter = 0, Function value 1.41775, Residual: 0.000342734 iter = 1, Function value 1.41775, Residual: 0.000275372 iter = 2, Function value 1.41775, Residual: 0.000148513 iter = 3, Function value 1.41775, Residual: 0.000150663 iter = 2, Function value 1.41775, Residual: < 1.0e-6 -- Stefano

1 0

Re: [petsc-dev] goggle still not good at finding petsc.org docs
by Patrick Sanan 12 Oct '21

12 Oct '21

For some reason for that term, Google returns a "petsc-3.5" URL instead of a "petsc-current" URL (which redirects). Maybe this was a problem even before we migrated to Sphinx? I don't have a great idea on how to fix, other than to slap a "THIS IS NOT CURRENT" label and a link on the top of all those pages (which is something nice to do, mimicking what Scikit-learn's website does). Re the search, it is indeed not rigged to search the man pages (or the HTML source), because those aren't fully integrated into Sphinx - they are generated by the "classic" process (involving configuring PETSc) and then copied into place. Maybe the most efficient way to resolve this is to push harder to make the man pages properly integrated into the Sphinx build. In the interest of making public the state of the docs more, I'm going to transfer the rest of my local notes to GitLab issues with the "doc" label (for this one, see #1015). Am Mo., 11. Okt. 2021 um 22:41 Uhr schrieb Barry Smith <bsmith(a)petsc.dev>: > > Googling TSTHETA leads to an ancient MCS page for the manual page not > to petsc.org > > > Searching for TSTHETA at petsc.org does not find the manual page; it > looks like the search is not rigged to search the manual pages? > > Barry > >

1 0

goggle still not good at finding petsc.org docs
by Barry Smith 11 Oct '21

11 Oct '21

Googling TSTHETA leads to an ancient MCS page for the manual page not to petsc.org Searching for TSTHETA at petsc.org <http://petsc.org/> does not find the manual page; it looks like the search is not rigged to search the manual pages? Barry

1 0

Re: [petsc-dev] Problem about DMPlexCreateExodusFromFile()
by Matthew Knepley 11 Oct '21

11 Oct '21

On Mon, Oct 11, 2021 at 9:29 AM Gong Yujie <yc17470(a)connect.um.edu.mo> wrote: > Hi, > > I'm learning PETSc DMPlex module recently. A problem occurs to my PETSc > when I'm using DMPlexCreateExodusFromFile() to import a mesh file. I've > tried to generate a mesh with Pointwise and ICEM, but both mesh files can't > be input to PETSc. The Error code is : > I am not familiar with Pointwise or ICEM. The problem here is that the element type 'TRIANGLE' is not recognized by PETSc, and it does not appear in the ExodusII documentation that I am using: https://gsjaardema.github.io/seacas-docs/html/element_types.html It is also not used by Cubit/Trellis. I am not sure why your program is making non-standard ExodusII files. Thanks, Matt > *[0]PETSC ERROR: --------------------- Error Message > --------------------------------------------------------------* > *[0]PETSC ERROR: Invalid argument* > *[0]PETSC ERROR: Unrecognized element type TRIANGLE* > *[0]PETSC ERROR: See https://petsc.org/release/faq/ > <https://petsc.org/release/faq/> for trouble shooting.* > *[0]PETSC ERROR: Petsc Release Version 3.16.0, Sep 29, 2021* > *[0]PETSC ERROR: ./exocircle on a arch-linux-c-debug named DESKTOP-0RMI66F > by fstcam Mon Oct 11 10:54:35 2021* > *[0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ > --with-fc=gfortran --download-mpich --download-fblaslapack --download-metis > --download-parmetis --download-exodusii --download-netcdf --download-hdf5 > --download-superlu --download-triangle --download-zlib --download-pnetcdf > --download-make --download-cmake* > *[0]PETSC ERROR: #1 ExodusGetCellType_Internal() at > /home/fstcam/petsc/petsc-3.16.0/src/dm/impls/plex/plexexodusii.c:1390[0]PETSC > ERROR: #2 DMPlexCreateExodus() at > /home/fstcam/petsc/petsc-3.16.0/src/dm/impls/plex/plexexodusii.c:1472* > *[0]PETSC ERROR: #3 DMPlexCreateExodusFromFile() at > /home/fstcam/petsc/petsc-3.16.0/src/dm/impls/plex/plexexodusii.c:1352* > > Looking forward to your reply! > > Best Regards, > Gong > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

1 0

Problem about DMPlexCreateExodusFromFile()
by Gong Yujie 11 Oct '21

11 Oct '21

Hi, I'm learning PETSc DMPlex module recently. A problem occurs to my PETSc when I'm using DMPlexCreateExodusFromFile() to import a mesh file. I've tried to generate a mesh with Pointwise and ICEM, but both mesh files can't be input to PETSc. The Error code is : [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Invalid argument [0]PETSC ERROR: Unrecognized element type TRIANGLE [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.16.0, Sep 29, 2021 [0]PETSC ERROR: ./exocircle on a arch-linux-c-debug named DESKTOP-0RMI66F by fstcam Mon Oct 11 10:54:35 2021 [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich --download-fblaslapack --download-metis --download-parmetis --download-exodusii --download-netcdf --download-hdf5 --download-superlu --download-triangle --download-zlib --download-pnetcdf --download-make --download-cmake [0]PETSC ERROR: #1 ExodusGetCellType_Internal() at /home/fstcam/petsc/petsc-3.16.0/src/dm/impls/plex/plexexodusii.c:1390[0]PETSC ERROR: #2 DMPlexCreateExodus() at /home/fstcam/petsc/petsc-3.16.0/src/dm/impls/plex/plexexodusii.c:1472 [0]PETSC ERROR: #3 DMPlexCreateExodusFromFile() at /home/fstcam/petsc/petsc-3.16.0/src/dm/impls/plex/plexexodusii.c:1352 Looking forward to your reply! Best Regards, Gong

1 0

Re: [petsc-dev] Question about the fully implicit Runge-Kutta methods (TS)
by Jed Brown 05 Oct '21

05 Oct '21

Matthew Knepley <knepley(a)gmail.com> writes: > On Tue, Oct 5, 2021 at 12:42 AM Wang Jingyuan <mc05569(a)connect.um.edu.mo> > wrote: > >> Dear Sir or Madam, >> >> I am a student of the University of Macau, I am trying to learn PETSc and >> I have two questions about the TSIRK. >> >> 1.PETSc 3.16.0 adds “irk" for the TSType and it offers many options like TSIRK1BEE, >> TSIRK2C, TSIRK2D, TSIRK2E, TSIRK3, TSIRKL2, >> > > The types you mention above do not exist. For instance, the first one > "TSIRK1BEE" is actually > https://petsc.org/main/docs/manualpages/TS/TSARKIMEX1BEE.html As Ed Bueler has commented, these non-existent types are incorrectly listed in the man page (people like me missed those copy/paste remnants during code review). https://petsc.org/main/docs/manualpages/TS/TSIRK.html The 1BEE and related types are diagonally implicit, so don't make sense under TSIRK. We would like to add Radau and Lobatto methods to PETSc -- it would be a relatively easy contribution.

1 0

Re: [petsc-dev] petsc-dev Digest, Vol 154, Issue 7
by Ed Bueler 05 Oct '21

05 Oct '21

The types listed by Wang Jing-Yuan are mentioned on https://petsc.org/main/docs/manualpages/TS/TSIRK.html So maybe they do exist, but I haven't tried them. TSARKIMEX are a better-tested alternative? Ed On Tue, Oct 5, 2021 at 2:44 AM <petsc-dev-request(a)mcs.anl.gov> wrote: > Send petsc-dev mailing list submissions to > petsc-dev(a)mcs.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.mcs.anl.gov/mailman/listinfo/petsc-dev > or, via email, send a message with subject or body 'help' to > petsc-dev-request(a)mcs.anl.gov > > You can reach the person managing the list at > petsc-dev-owner(a)mcs.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of petsc-dev digest..." > > > Today's Topics: > > 1. Question about the fully implicit Runge-Kutta methods (TS) > (Wang Jingyuan) > 2. Re: Question about the fully implicit Runge-Kutta methods > (TS) (Matthew Knepley) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 5 Oct 2021 03:56:48 +0000 > From: Wang Jingyuan <mc05569(a)connect.um.edu.mo> > To: "petsc-dev(a)mcs.anl.gov" <petsc-dev(a)mcs.anl.gov> > Subject: [petsc-dev] Question about the fully implicit Runge-Kutta > methods (TS) > Message-ID: <3CE2CAF7-35EC-44E9-AE78-856BEF270AA2(a)connect.umac.mo> > Content-Type: text/plain; charset="utf-8" > > Dear Sir or Madam, > > I am a student of the University of Macau, I am trying to learn PETSc and > I have two questions about the TSIRK. > > 1.PETSc 3.16.0 adds ?irk" for the TSType and it offers many options like > TSIRK1BEE, TSIRK2C, TSIRK2D, TSIRK2E, TSIRK3, TSIRKL2, I am not sure how > to use them and if only Gaussian points can be used (Radau or Labatto may > not offered). > > 2.Maybe there is a similar option to implement the fully implicit > Runge-Kutta methods in PETSc 3.15 or other previous versions? For example, > if I want to solve a time dependent problem with a butcher table like > below, do I need to input it by myself? > [cid:CF3DAFB6-6115-45C2-BEE4-0ADCA66709BB] > > Thank you very much for your help. > > Best regards, > Wang Jing-Yuan >

1 0

Re: [petsc-dev] Question about the fully implicit Runge-Kutta methods (TS)
by Matthew Knepley 05 Oct '21

05 Oct '21

On Tue, Oct 5, 2021 at 12:42 AM Wang Jingyuan <mc05569(a)connect.um.edu.mo> wrote: > Dear Sir or Madam, > > I am a student of the University of Macau, I am trying to learn PETSc and > I have two questions about the TSIRK. > > 1.PETSc 3.16.0 adds “irk" for the TSType and it offers many options like TSIRK1BEE, > TSIRK2C, TSIRK2D, TSIRK2E, TSIRK3, TSIRKL2, > The types you mention above do not exist. For instance, the first one "TSIRK1BEE" is actually https://petsc.org/main/docs/manualpages/TS/TSARKIMEX1BEE.html > I am not sure how to use them and if only Gaussian points can be used > (Radau or Labatto may not offered). > There is currently only one IRK type, which is the Gauss method. > 2.Maybe there is a similar option to implement the fully implicit > Runge-Kutta methods in PETSc 3.15 or other previous versions? For example, > if I want to solve a time dependent problem with a butcher table like > below, do I need to input it by myself? > > Thank you very much for your help. > I do not understand your question. IRK is only present is 3.16 Thanks, Matt > Best regards, > Wang Jing-Yuan > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>

1 0

Question about the fully implicit Runge-Kutta methods (TS)
by Wang Jingyuan 04 Oct '21

04 Oct '21

Dear Sir or Madam, I am a student of the University of Macau, I am trying to learn PETSc and I have two questions about the TSIRK. 1.PETSc 3.16.0 adds “irk" for the TSType and it offers many options like TSIRK1BEE, TSIRK2C, TSIRK2D, TSIRK2E, TSIRK3, TSIRKL2, I am not sure how to use them and if only Gaussian points can be used (Radau or Labatto may not offered). 2.Maybe there is a similar option to implement the fully implicit Runge-Kutta methods in PETSc 3.15 or other previous versions? For example, if I want to solve a time dependent problem with a butcher table like below, do I need to input it by myself? [cid:CF3DAFB6-6115-45C2-BEE4-0ADCA66709BB] Thank you very much for your help. Best regards, Wang Jing-Yuan

1 0

Why clanguage __str1__ appears before the summary?
by Stefano Zampini 03 Oct '21

03 Oct '21

at the end, configure dumps the summary. The c language used should appear in the PETSc: section of the summary, but it is actually printed before ... regex: Language used to compile PETSc: C PETSc: PETSC_ARCH: arch-wtf .... -- Stefano

1 0